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Vigil K, D'Souza N, Bazner J, Cedraz FMA, Fisch S, Rose JB, Aw TG. Long-term monitoring of SARS-CoV-2 variants in wastewater using a coordinated workflow of droplet digital PCR and nanopore sequencing. WATER RESEARCH 2024; 254:121338. [PMID: 38430753 DOI: 10.1016/j.watres.2024.121338] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 02/12/2024] [Accepted: 02/17/2024] [Indexed: 03/05/2024]
Abstract
Quantitative polymerase chain reaction (PCR) and genome sequencing are important methods for wastewater surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The reverse transcription-droplet digital PCR (RT-ddPCR) is a highly sensitive method for quantifying SARS-CoV-2 RNA in wastewater samples to track the trends of viral activity levels but cannot identify new variants. It also takes time to develop new PCR-based assays targeting variants of interest. Whole genome sequencing (WGS) can be used to monitor known and new SARS-CoV-2 variants, but it is generally not quantitative. Several short-read sequencing techniques can be expensive and might experience delayed turnaround times when outsourced due to inadequate in-house resources. Recently, a portable nanopore sequencing system offers an affordable and real-time method for sequencing SARS-CoV-2 variants in wastewater. This technology has the potential to enable swift response to disease outbreaks without relying on clinical sequencing results. In addressing concerns related to rapid turnaround time and accurate variant analysis, both RT-ddPCR and nanopore sequencing methods were employed to monitor the emergence of SARS-CoV-2 variants in wastewater. This surveillance was conducted at 23 sewer maintenance hole sites and five wastewater treatment plants in Michigan from 2020 to 2022. In 2020, the wastewater samples were dominated by the parental variants (20A, 20C and 20 G), followed by 20I (Alpha, B.1.1.7) in early 2021 and the Delta variant of concern (VOC) in late 2021. For the year 2022, Omicron variants dominated. Nanopore sequencing has the potential to validate suspected variant cases that were initially undetermined by RT-ddPCR assays. The concordance rate between nanopore sequencing and RT-ddPCR assays in identifying SARS-CoV-2 variants to the clade-level was 76.9%. Notably, instances of disagreement between the two methods were most prominent in the identification of the parental and Omicron variants. We also showed that sequencing wastewater samples with SARS-CoV-2 N gene concentrations of >104 GC/100 ml as measured by RT-ddPCR improve genome recovery and coverage depth using MinION device. RT-ddPCR was better at detecting key spike protein mutations A67V, del69-70, K417N, L452R, N501Y, N679K, and R408S (p-value <0.05) as compared to nanopore sequencing. It is suggested that RT-ddPCR and nanopore sequencing should be coordinated in wastewater surveillance where RT-ddPCR can be used as a preliminary quantification method and nanopore sequencing as the confirmatory method for the detection of variants or identification of new variants. The RT-ddPCR and nanopore sequencing methods reported here can be adopted as a reliable in-house analysis of SARS-CoV-2 in wastewater for rapid community level surveillance and public health response.
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Affiliation(s)
- Katie Vigil
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 2100, New Orleans, LA 70112, United States
| | - Nishita D'Souza
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, United States
| | - Julia Bazner
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, United States
| | - Fernanda Mac-Allister Cedraz
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 2100, New Orleans, LA 70112, United States
| | - Samuel Fisch
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 2100, New Orleans, LA 70112, United States
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, United States
| | - Tiong Gim Aw
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 2100, New Orleans, LA 70112, United States.
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2
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Ode H, Nakata Y, Nagashima M, Hayashi M, Yamazaki T, Asakura H, Suzuki J, Kubota M, Matsuoka K, Matsuda M, Mori M, Sugimoto A, Imahashi M, Yokomaku Y, Sadamasu K, Iwatani Y. Molecular-Epidemiological Features of SARS-CoV-2 in Japan, 2020-2021. Virus Evol 2022; 8:veac034. [PMID: 35478716 PMCID: PMC9037363 DOI: 10.1093/ve/veac034] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/12/2022] [Accepted: 04/07/2022] [Indexed: 11/24/2022] Open
Abstract
There were five epidemic waves of coronavirus disease 2019 in Japan between 2020 and 2021. It remains unclear how the domestic waves arose and abated. To better understand this, we analyzed the pangenomic sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and characterized the molecular epidemiological features of the five epidemic waves in Japan. In this study, we performed deep sequencing to determine the pangenomic SARS-CoV-2 sequences of 1,286 samples collected in two cities far from each other, Tokyo Metropolis and Nagoya. Then, the spatiotemporal genetic changes of the obtained sequences were compared with the sequences available in the Global Initiative on Sharing All Influenza Data (GISAID) database. A total of 873 genotypes carrying different sets of mutations were identified in the five epidemic waves. Phylogenetic analysis demonstrated that sharp displacements of lineages and genotypes occurred between consecutive waves over the 2 years. In addition, a wide variety of genotypes were observed in the early half of each wave, whereas a few genotypes were detected across Japan during an entire wave. Phylogenetically, putative descendant genotypes observed late in each wave displayed regional clustering and evolution in Japan. The genetic diversity of SARS-CoV-2 displayed uneven dynamics during each epidemic wave in Japan. Our findings provide an important molecular epidemiological basis to aid in controlling future SARS-CoV-2 epidemics.
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Affiliation(s)
- Hirotaka Ode
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya 460-0001, Japan
| | - Yoshihiro Nakata
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya 460-0001, Japan
- Division of Basic Medicine, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Mami Nagashima
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo169-0073, Japan
| | - Masaki Hayashi
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo169-0073, Japan
| | - Takako Yamazaki
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo169-0073, Japan
| | - Hiroyuki Asakura
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo169-0073, Japan
| | - Jun Suzuki
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo169-0073, Japan
| | - Mai Kubota
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya 460-0001, Japan
| | - Kazuhiro Matsuoka
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya 460-0001, Japan
| | - Masakazu Matsuda
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya 460-0001, Japan
| | - Mikiko Mori
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya 460-0001, Japan
- Division of Basic Medicine, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Atsuko Sugimoto
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya 460-0001, Japan
| | - Mayumi Imahashi
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya 460-0001, Japan
| | - Yoshiyuki Yokomaku
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya 460-0001, Japan
| | - Kenji Sadamasu
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo169-0073, Japan
| | - Yasumasa Iwatani
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya 460-0001, Japan
- Division of Basic Medicine, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
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Kawasaki H, Suzuki H, Furuhashi K, Yamashita K, Ishikawa J, Nagura O, Maekawa M, Miwa T, Tandou T, Hariyama T. Highly Sensitive and Quantitative Diagnosis of SARS-CoV-2 Using a Gold/Platinum Particle-Based Lateral Flow Assay and a Desktop Scanning Electron Microscope. Biomedicines 2022; 10:biomedicines10020447. [PMID: 35203656 PMCID: PMC8962435 DOI: 10.3390/biomedicines10020447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/04/2022] [Accepted: 02/05/2022] [Indexed: 12/23/2022] Open
Abstract
The gold standard test for identifying SARS-CoV-2, the causative agent of COVID-19, is polymerase chain reaction (PCR). Despite their limited sensitivity, SARS-CoV-2 antigen rapid diagnostic tests are vital tools in the fight against viral spread. Owing to its simplicity and low cost, the lateral flow assay (LFA) is the most extensively used point-of-care diagnostic test. Here, we report a newly designed LFA-NanoSuit method (LNSM) that works in conjunction with desktop scanning electron microscopy (SEM) to detect SARS-CoV-2. LNSM requires no standard SEM treatment, avoids cellulose and residual buffer deformation, and enables the capture of high-resolution images of antibody-labeled gold/platinum particles reacting with SARS-CoV-2 antigens. To assess its applicability, we compared clinical SARS-CoV-2 samples via visual detection of LFA, LSNM detection of LFA, and real-time reverse transcription-PCR (qRT-PCR). Compared to qRT-PCR, LNSM showed 86.7% sensitivity (26/30; 95% confidence interval (CI): 69.28–96.24%) and 93.3% specificity (14/15; 95% CI: 68.05–99.83%) for SARS-CoV-2. In samples with a relatively low SARS-CoV-2 RNA copy number (30 < Ct ≤ 40), the sensitivity of LNSM was greater (73.3%) than that of visual detection (0%). A simple, sensitive, and quantitative LNSM can be used to diagnose SARS-CoV-2.
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Affiliation(s)
- Hideya Kawasaki
- Institute for NanoSuit Research, Preeminent Medical Photonics Education & Research Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan; (H.S.); (T.H.)
- Correspondence: ; Tel.: +81-53-435-2504
| | - Hiromi Suzuki
- Institute for NanoSuit Research, Preeminent Medical Photonics Education & Research Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan; (H.S.); (T.H.)
| | - Kazuki Furuhashi
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan; (K.F.); (K.Y.); (J.I.); (O.N.); (M.M.)
| | - Keita Yamashita
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan; (K.F.); (K.Y.); (J.I.); (O.N.); (M.M.)
| | - Jinko Ishikawa
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan; (K.F.); (K.Y.); (J.I.); (O.N.); (M.M.)
| | - Osanori Nagura
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan; (K.F.); (K.Y.); (J.I.); (O.N.); (M.M.)
| | - Masato Maekawa
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan; (K.F.); (K.Y.); (J.I.); (O.N.); (M.M.)
| | - Takafumi Miwa
- Research & Development Group, Hitachi Ltd., 1-280, Higashi-Koigakubo, Kokubunji-shi, Tokyo 185-8601, Japan;
| | - Takumi Tandou
- Social Solution Department, Hitachi Social Information Services Ltd., Omori Bellport D 17F, 6-26-3, Minamioi, Shinagawa-ku, Tokyo 140-0013, Japan;
| | - Takahiko Hariyama
- Institute for NanoSuit Research, Preeminent Medical Photonics Education & Research Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan; (H.S.); (T.H.)
- NanoSuit Inc., 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan
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Aoki K, Takai K, Nagasawa T, Kashiwagi K, Mori N, Matsubayashi K, Satake M, Tanaka I, Kodama N, Shimodaira T, Ishii Y, Miyazaki T, Ishii T, Morita T, Yoshimura T, Tateda K. Combination of a SARS-CoV-2 IgG Assay and RT-PCR for Improved COVID-19 Diagnosis. Ann Lab Med 2021; 41:568-576. [PMID: 34108284 PMCID: PMC8203440 DOI: 10.3343/alm.2021.41.6.568] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/11/2020] [Accepted: 05/10/2021] [Indexed: 01/08/2023] Open
Abstract
Background Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is generally diagnosed by reverse transcription (RT)-PCR or serological assays. The SARS-CoV-2 viral load decreases a few days after symptom onset. Thus, the RT-PCR sensitivity peaks at three days after symptom onset (approximately 80%). We evaluated the performance of the ARCHITECT® SARS-CoV-2 IgG assay (henceforth termed IgG assay; Abbott Laboratories, Lake County, IL, USA), and the combination of RT-PCR and the IgG assay for COVID-19 diagnosis. Methods In this retrospective study, 206 samples from 70 COVID-19 cases at two hospitals in Tokyo that were positive using RT-PCR were used to analyze the diagnostic sensitivity. RT-PCR-negative (N=166), COVID-19-unrelated (N=418), and Japanese Red Cross Society (N=100) samples were used to evaluate specificity. Results Sensitivity increased daily after symptom onset and exceeded 84.4% after 10 days. Specificity ranged from 98.2% to 100% for samples from the three case groups. Seroconversion was confirmed from 9 to 20 days after symptom onset in 18 out of 32 COVID-19 cases with multiple samples and from another case with a positive result in the IgG assay for the first available sample. Conclusions The combination of RT-PCR and IgG assay improves the robustness of laboratory diagnostics by compensating for the limitations of each method.
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Affiliation(s)
- Kotaro Aoki
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Kunitomo Takai
- Research and Development, Abbott Japan LLC, Chiba, Japan
| | - Tatsuya Nagasawa
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Katsuhito Kashiwagi
- General Medicine and Emergency Center (Internal Medicine), Toho University Omori Medical Center, Tokyo, Japan
| | - Nobuaki Mori
- Department of General Internal Medicine and Infectious Diseases, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Keiji Matsubayashi
- Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Masahiro Satake
- Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Ippei Tanaka
- Research and Development, Abbott Japan LLC, Chiba, Japan
| | - Nanae Kodama
- Department of Clinical Laboratory, Toho University Omori Medical Center, Tokyo, Japan
| | - Takahiro Shimodaira
- Department of Clinical Laboratory, Toho University Omori Medical Center, Tokyo, Japan
| | - Yoshikazu Ishii
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Taito Miyazaki
- General Medicine and Emergency Center (Internal Medicine), Toho University Omori Medical Center, Tokyo, Japan
| | - Toshiaki Ishii
- Department of Clinical Laboratory, Toho University Omori Medical Center, Tokyo, Japan
| | - Toshisuke Morita
- Department of Laboratory Medicine, Toho University School of Medicine, Tokyo, Japan
| | - Toru Yoshimura
- Research and Development, Abbott Japan LLC, Chiba, Japan
| | - Kazuhiro Tateda
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
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5
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Akiyama Y, Kinoshita N, Sadamasu K, Nagashima M, Yoshida I, Kusaba Y, Suzuki T, Nagashima M, Ishikane M, Takasaki J, Yoshimura K, Ohmagari N. A pilot study of viral load in stools of patients with COVID-19 and diarrhea. Jpn J Infect Dis 2021; 75:36-40. [PMID: 34053956 DOI: 10.7883/yoken.jjid.2021.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
It is known that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be detected in the stools of patients with the coronavirus disease 2019 (COVID-19) and that the virus can be transmitted by oral-fecal route. However, there are few reports on the viral load in stools. This pilot study aimed to evaluate the clinical characteristics and viral load of SARS-CoV-2 in the stools of 13 patients with confirmed COVID-19 using as control the pepper mild mottle virus, which was proposed as a potential indicator of human fecal contamination of environmental water. SARS-CoV-2 RNA was detected in stool samples from four patients (31%), among whom three presented diarrhea symptoms. One patient experiencing long-term diarrhea (22 days) had high levels of viral RNA in the stools (8.28 log10 copies/g). However, we could not isolate the SARS-CoV-2 in the stool of any patients, using VeroE6/TMPRESS2 cells for four weeks. Our results suggest that SARS-CoV-2 RNA may be detected in the stools of patients with the diarrhea symptoms. Further studies evaluating the relationship between SARS-CoV-2 viral load in stools and diarrhea symptoms in larger patient cohorts and upon adjusting for other causative factors and virus infectivity are still needed.
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Affiliation(s)
- Yutaro Akiyama
- Department of Infectious Diseases, Disease Control and Prevention Center, National Center for Global Health and Medicine, Japan
| | - Noriko Kinoshita
- Department of Infectious Diseases, Disease Control and Prevention Center, National Center for Global Health and Medicine, Japan
| | - Kenji Sadamasu
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Japan
| | - Mami Nagashima
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Japan
| | - Isao Yoshida
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Japan
| | - Yusaku Kusaba
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Japan
| | - Tetsuya Suzuki
- Department of Infectious Diseases, Disease Control and Prevention Center, National Center for Global Health and Medicine, Japan
| | - Maki Nagashima
- Department of Infectious Diseases, Disease Control and Prevention Center, National Center for Global Health and Medicine, Japan
| | - Masahiro Ishikane
- Department of Infectious Diseases, Disease Control and Prevention Center, National Center for Global Health and Medicine, Japan
| | - Jin Takasaki
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Japan
| | - Kazuhisa Yoshimura
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Japan
| | - Norio Ohmagari
- Department of Infectious Diseases, Disease Control and Prevention Center, National Center for Global Health and Medicine, Japan
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6
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Nomoto H, Ishikane M, Katagiri D, Kinoshita N, Nagashima M, Sadamasu K, Yoshimura K, Ohmagari N. Cautious handling of urine from moderate to severe COVID-19 patients. Am J Infect Control 2020; 48:969-971. [PMID: 32502614 PMCID: PMC7266575 DOI: 10.1016/j.ajic.2020.05.034] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 05/28/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Hidetoshi Nomoto
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan; Collaborative Chairs Emerging and Reemerging Infectious Diseases, National Center for Global Health and Medicine, Graduate School of Medicine, Tohoku University, Sendai city, Miyagi, Japan
| | - Masahiro Ishikane
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan; AMR Clinical Reference Center, Disease Control and Prevention Center, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan.
| | - Daisuke Katagiri
- Department of Nephrology, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Noriko Kinoshita
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan; Collaborative Chairs Emerging and Reemerging Infectious Diseases, National Center for Global Health and Medicine, Graduate School of Medicine, Tohoku University, Sendai city, Miyagi, Japan
| | - Mami Nagashima
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Shinjuku-ku, Tokyo, Japan
| | - Kenji Sadamasu
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Shinjuku-ku, Tokyo, Japan
| | - Kazuhisa Yoshimura
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Shinjuku-ku, Tokyo, Japan
| | - Norio Ohmagari
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan; Collaborative Chairs Emerging and Reemerging Infectious Diseases, National Center for Global Health and Medicine, Graduate School of Medicine, Tohoku University, Sendai city, Miyagi, Japan; AMR Clinical Reference Center, Disease Control and Prevention Center, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
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